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Crystal structure of bacillithiol methyltransferase NmbA from Chlorobaculum tepidum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold Q8KDK7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.6 298 13 mg/mL protein (1:1) 0.03 M citric acid, 0.07 M BIS-TRIS propane, pH = 7.6, 20 % w/v polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.65 53.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.751 α = 90 b = 55.517 β = 90 c = 186.017 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 X 9M 2022-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9184 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.7 47.67 97 0.228 0.256 0.114 0.981 6.3 4.9 15493 48.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.83 97 1.23 1.382 0.617 0.455 1.3 4.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.7 47.67 1.34 15427 778 96.46 0.2147 0.2127 0.2117 0.2529 0.2513 52.68
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.5127 f_angle_d 0.5561 f_chiral_restr 0.042 f_plane_restr 0.0056 f_bond_d 0.0024
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3682 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 45
Software Software Software Name Purpose PHENIX refinement REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing